Perl Script For Blast+

Question

[H@rry]

Hi, how can I blast using perl script as I have whole database i.e subject with me and a single protein file is arranged in FASTA format. I have used Blast+ for the creation of database and have three file .psq, .pin, and phr, for the same and wish to obtain the results of all the query sequences in one file. Please suggest some script as I am new in perl.

thank you in advance.

Answer 1

[Daniel]

You don't need to use perl (or any other language) for this, just call blast+ as it is

Tutorials like this will help: https://molevol.mbl.edu/wiki/index.php/BLAST_UNIX_Tutorial

[H@rry]

Thanks a ton..it works fine ...

Answer 2

[vijay]

You can use the system or the exec command. The basic syntax is as below. Please note that you keep the blast executable file in the same folder as your perl scripts.

system("blastn -query $inputfile -db $db-name -evalue $evalue -out output_filename");